[gmx-users] energy minimization

[Dallas Warren]

Look around atom 2016, there is a bad contact between the atoms in that
area, hence the infinite force, very high potential energy, and the
minimisation fails.

On Tue, 25 Sep. 2018, 6:48 pm ikjk, <1761440083 at qq.com> wrote:

> hello
>    I am doing a md with martini force filed,I create a box, there is a
> double monolayer, then I solvate it, but when I did energy minimization,
>
> gmx grompp -f minim.mdp -c solv.gro -p dppc.top -o em.tpr          then
>
> NOTE 1 [file minim.mdp]:
>   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>   that with the Verlet scheme, nstlist has no effect on the accuracy of
>   your simulation.
>
> Setting the LD random seed to 562058480
> Generated 0 of the 780 non-bonded parameter combinations
> Excluding 1 bonded neighbours molecule type 'DPPC'
> Excluding 1 bonded neighbours molecule type 'W'
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are: 72143      Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 261042.00
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 168x168x208, spacing 0.118 0.118 0.118
>                                 Estimate for the relative computational
> load of the PME mesh part: 0.91
>
> NOTE 2 [file minim.mdp]:
>   The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid spacing.
>
>
>
>
>
>
>
>
> gmx mdrun -v -deffnm em
>
>
>
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+03
>    Number of steps    =        50000
> Step=   14, Dmax= 1.2e-06 nm, Epot=  2.36880e+22 Fmax=         inf, atom=
> 2016
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 1000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
>
> writing lowest energy coordinates.
> it just stopped with 14 steps, here is my mdp file,if you can solve this
> problem, I will appreciate that.
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator  = steep         ; Algorithm (steep = steepest descent
> minimization)
> emtol       = 1000.0        ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep      = 0.01          ; Minimization step size
> nsteps      = 50000         ; Maximum number of (minimization) steps to
> perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist         = 1         ; Frequency to update the neighbor list and
> long range forces
> cutoff-scheme   = Verlet    ; Buffered neighbor searching
> ns_type         = grid      ; Method to determine neighbor list (simple,
> grid)
> coulombtype     = PME       ; Treatment of long range electrostatic
> interactions
> rcoulomb        = 1.0       ; Short-range electrostatic cut-off
> rvdw            = 1.0       ; Short-range Van der Waals cut-off
> pbc             = xyz       ; Periodic Boundary Conditions in all 3
> dimensions
>
>
>
>
>
>
>
>
> jiao
> --
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